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Long non-coding mRNA

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https://www.readbyqxmd.com/read/28337266/long-non-coding-rna-uca1-promotes-cell-progression-by-acting-as-a-competing-endogenous-rna-of-atf2-in-prostate-cancer
#1
Shilong Zhang, Xinxin Dong, Tongyu Ji, Guoxiao Chen, Lei Shan
Prostate cancer (PCa) is a leading cause of cancer-related deaths in elder men. This disease has limited therapeutic options and poor prognosis as the underlying molecular mechanisms are not clearly understood. LncRNA UCA1 functions as an oncogene in many types of cancers. However, the role of UCA1 in PCa remains unclear. In the present study, we showed that UCA1 was significantly up-regulated in PCa cell lines and tissue samples. High UCA1 expression was positively associated with high gleason score, advanced TNM stage and shorter overall survival of PCa patients...
2017: American Journal of Translational Research
https://www.readbyqxmd.com/read/28335026/melting-temperature-highlights-functionally-important-rna-structure-and-sequence-elements-in-yeast-mrna-coding-regions
#2
Fei Qi, Dmitrij Frishman
Secondary structure elements in the coding regions of mRNAs play an important role in gene expression and regulation, but distinguishing functional from non-functional structures remains challenging. Here we investigate the dependence of sequence-structure relationships in the coding regions on temperature based on the recent PARTE data by Wan et al. Our main finding is that the regions with high and low thermostability (high Tm and low Tm regions) are under evolutionary pressure to preserve RNA secondary structure and primary sequence, respectively...
March 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28331188/seven-lncrna-mrna-based-risk-score-predicts-the-survival-of-head-and-neck-squamous-cell-carcinoma
#3
Zhi-Li Zhang, Li-Jing Zhao, Liang Chai, Shui-Hong Zhou, Feng Wang, Yan Wei, Ya-Ping Xu, Peng Zhao
Dysregulation of mRNAs and long non-coding RNAs (lncRNAs) is one of the most important features of carcinogenesis and cancer development. However, studies integrating the expression of mRNAs and lncRNAs to predict the survival of head and neck squamous cell carcinoma (HNSC) are still limited, hitherto. In current work, we identified survival related mRNAs and lncRNAs in three datasets (TCGA dataset, E-TABM-302, GSE41613). By random forest, seven gene signatures (six mRNAs and lncRNA) were further selected to develop the risk score model...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28320503/post-transcriptional-and-translational-regulation-of-mrna-like-long-non-coding-rnas-by-micrornas-in-early-developmental-stages-of-zebrafish-embryos
#4
Kyung-Tae Lee, Jin-Wu Nam
microRNA (miRNA) represses protein-coding gene via seed pairing to 3' untranslated reiongs (UTRs) of mRNA at the post-transcriptional and translational level. Although working models of miRNA-mediated gene silencing have been successfully established using miRNA transfections and knockouts, the regulatory interaction between miRNA and long non-coding RNA (lncRNA) remain unknown. In particular, how mRNA-resembling lncRNAs with 5' cap, 3' poly(A)-tail, or coding features are regulated by miRNA is yet to be examined...
March 21, 2017: BMB Reports
https://www.readbyqxmd.com/read/28316063/endothelial-long-non-coding-rnas-regulated-by-oxidized-ldl
#5
Krishna K Singh, Pratiek N Matkar, Yi Pan, Adrian Quan, Vijay Gupta, Hwee Teoh, Mohammed Al-Omran, Subodh Verma
Oxidized low-density lipoprotein (oxLDL) plays a central role in the pathogenesis of atherosclerosis, in part via an effect to promote endothelial dysfunction. In the present study, we evaluated the expression profiles of long non-coding RNAs (lncRNAs) and protein-coding mRNAs in endothelial cells following oxLDL stimulation. LncRNAs and mRNAs from human umbilical vein endothelial cells (HUVECs) were profiled with the Arraystar Human lncRNA Expression Microarray V3.0 following 24 h of oxLDL treatment (100 µg/mL)...
March 18, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28304380/comprehensive-analysis-of-the-cancer-genome-atlas-reveals-a-unique-gene-and-non-coding-rna-signature-of-fibrolamellar-carcinoma
#6
Timothy A Dinh, Eva C M Vitucci, Eliane Wauthier, Rondell P Graham, Wendy A Pitman, Tsunekazu Oikawa, Mengjie Chen, Grace O Silva, Kevin G Greene, Michael S Torbenson, Lola M Reid, Praveen Sethupathy
Fibrolamellar carcinoma (FLC) is a unique liver cancer primarily affecting young adults and characterized by a fusion event between DNAJB1 and PRKACA. By analyzing RNA-sequencing data from The Cancer Genome Atlas (TCGA) for >9,100 tumors across ~30 cancer types, we show that the DNAJB1-PRKACA fusion is specific to FLCs. We demonstrate that FLC tumors (n = 6) exhibit distinct messenger RNA (mRNA) and long intergenic non-coding RNA (lincRNA) profiles compared to hepatocellular carcinoma (n = 263) and cholangiocarcinoma (n = 36), the two most common liver cancers...
March 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28299977/identification-of-lymph-node-metastasis-related-micrornas-in-lung-adenocarcinoma-and-analysis-of-the-underlying-mechanisms-using-a-bioinformatics-approach
#7
Li Yan, Demin Jiao, Huizhen Hu, Jian Wang, Xiali Tang, Jun Chen, Qingyong Chen
This study aimed to screen lymphatic metastasis-related microRNAs (miRNAs) in lung adenocarcinoma and explore their underlying mechanisms using bioinformatics. The miRNA expression in primary lung adenocarcinoma, matched adjacent non-tumorigenic and lymph node metastasis tissues of patients were profiled via microarray. The screened metastasis-related miRNAs were then validated using quantitative real-time PCR in a second cohort of lung adenocarcinoma patients with lymphatic metastasis. Significance was determined using a paired t-test...
April 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28295592/knockdown-of-long-non-coding-rna-zfas1-protects-cardiomyocytes-against-acute-myocardial-infarction-via-anti-apoptosis-by-regulating-mir-150-crp
#8
Tao Wu, Dan Wu, Qinghua Wu, Bing Zou, Xiao Huang, Xiaoshu Cheng, Yanqing Wu, Kui Hong, Ping Li, Renqiang Yang, Yunde Li, Yingzhang Cheng
BACKGROUND: ZFAS1 is one of cardiac-specific or cardiac-related lncRNAs. This study was to explore the functional involvement of ZFAS1 and its regulatory role in AMI. METHODS: In this study, the models of AMI rat and myocardial cell cultured under hypoxia were made. The expression of ZFAS1 and miR-150 of myocardial infarction tissue or cardiac myocytes was determined by quantitative real time PCR. The regulatory role of ZFAS1 on miR-150 was examined by RNA pull down assay...
March 10, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28291811/systematic-identification-and-characterization-of-long-non-coding-rnas-in-mouse-mature-sperm
#9
Xiaoning Zhang, Fengxin Gao, Jianbo Fu, Peng Zhang, Yuqing Wang, Xuhui Zeng
Increasing studies have shown that mature spermatozoa contain many transcripts including mRNAs and miRNAs. However, the expression profile of long non-coding RNAs (lncRNAs) in mammalian sperm has not been systematically investigated. Here, we used highly purified RNA to investigate lncRNA expression profiles in mouse mature sperm by stranded-specific RNA-seq. We identified 20,907 known and 4,088 novel lncRNAs transcripts, and the existence of intact lncRNAs was confirmed by RT-PCR and fluorescence in situ hybridization on two representative lncRNAs...
2017: PloS One
https://www.readbyqxmd.com/read/28288210/depletion-of-neat1-lncrna-attenuates-nucleolar-stress-by-releasing-sequestered-p54nrb-and-psf-to-facilitate-c-myc-translation
#10
Wen Shen, Xue-Hai Liang, Hong Sun, Cheryl L De Hoyos, Stanley T Crooke
Altered expression of NEAT1, the architectural long non-coding RNA (lncRNA) of nuclear paraspeckles, has been reported during tumorigenesis, as well as under various cellular stress conditions. Here we report that the depletion of NEAT1 lncRNA alleviates nucleolar stress during RNAP I inhibition through releasing sequestered P54nrb and PSF to facilitate the IRES-dependent translation of c-Myc. RNAP I inhibitor CX5461 disrupts the SL1-rDNA interaction and induces nucleolar disruption, demonstrated by the accumulation of fibrillarin-containing nucleoplasmic foci and nucleolar clearance of ribosomal proteins in HeLa cells...
2017: PloS One
https://www.readbyqxmd.com/read/28286086/hyper-methylation-of-the-upstream-cpg-island-shore-is-a-likely-mechanism-of-gper1-silencing-in-breast-cancer-cells
#11
Mohan C Manjegowda, Paridhi Singhal Gupta, Anil M Limaye
GPER1, also known as GPR30, is a novel seven-transmembrane G-protein coupled estrogen receptor that mediates both short-term (non-genomic) and long-term (genomic) effects of estrogen in target cells and tissues. A substantial body of work over the last two decades has highlighted its therapeutic or prognostic utility. However, the clinical data on the expression of GPER1 in breast tissue is ambiguous. Analysis of TCGA RNAseq data revealed significantly lower mean expression of GPER1 mRNA in primary breast tumors compared to that in normal breast tissues...
March 7, 2017: Gene
https://www.readbyqxmd.com/read/28282787/long-non-coding-rna-snhg20-predicts-a-poor-prognosis-for-hcc-and-promotes-cell-invasion-by-regulating-the-epithelial-to-mesenchymal-transition
#12
Jinxia Liu, Cuihua Lu, Mingbing Xiao, Feng Jiang, Lishuai Qu, Runzhou Ni
BACKGROUND: Recently, Accumulating evidence indicates that long noncoding RNAs (lncRNAs) have been shown to have critical regulatory roles in human tumor biology and development. However, the expression pattern and biological function of lncRNA small nucleolar RNA host gene 20 (SNHG20) in hepatocellular carcinoma (HCC) remains largely unknown. METHODS: The expression of SNHG20 in 96 paired HCC tissues and cell lines were detected by quantitative real-time PCR (qRT-PCR) analysis...
March 6, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28276823/the-role-of-malat-1-in-the-invasion-and-metastasis-of-gastric-cancer
#13
Di Chen, Lili Liu, Kai Wang, Haiyan Yu, Yafang Wang, Jiaming Liu, Yang Guo, Hongbo Zhang
OBJECTIVES: The long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT-1) has been reported to be over-expressed in several cancer types. However, its role in gastric cancer (GC) remains unclear. In the present study, we examined the expression of MALAT-1 in GC cells and tissues and explored its role in GC cell migration and invasion. MATERIALS AND METHODS: Real-time quantitative polymerase chain reaction (qRT-PCR) was used to analyze the expression level of MALAT-1 in six GC cell lines and 20 gastric tissues (20 GC and 20 adjacent normal mucosa)...
March 1, 2017: Scandinavian Journal of Gastroenterology
https://www.readbyqxmd.com/read/28275212/long-non-coding-rna-profiling-in-a-non-alcoholic-fatty-liver-disease-rodent-model-new-insight-into-pathogenesis
#14
Yi Chen, Haixiu Huang, Chengfu Xu, Chaohui Yu, Youming Li
Non-alcoholic fatty liver disease (NAFLD) is one of the most prevalent chronic liver diseases worldwide with an unclear mechanism. Long non-coding RNAs (lncRNAs) have recently emerged as important regulatory molecules. To better understand NAFLD pathogenesis, lncRNA and messenger RNA (mRNA) microarrays were conducted in an NAFLD rodent model. Potential target genes of significantly changed lncRNA were predicted using cis/trans-regulatory algorithms. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were then performed to explore their function...
January 16, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28272713/long-non-coding-rna-ccat2-promotes-the-breast-cancer-growth-and-metastasis-by-regulating-tgf-%C3%AE-signaling-pathway
#15
Z-J Wu, Y Li, Y-Z Wu, Y Wang, W-Q Nian, L-L Wang, L-C Li, H-L Luo, D-L Wang
OBJECTIVE: Long non-coding RNA (LncRNA) CCAT2 plays an important role in tumorigenesis, tumor growth and metastasis. In this study, we reported that long noncoding RNA CCAT2 (LncRNA CCAT2) could regulate TGF-β signaling pathway in breast cancer. PATIENTS AND METHODS: The relative mRNA expression level of CCAT2 in adjacent non-cancerous and breast cancer tissues without or with metastasis were analyzed by quantitative Real-time polymerase chain reaction (qRT-PCR)...
February 2017: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/28269753/lncrna-neat1-is-a-prognosis-biomarker-and-regulates-cancer-progression-via-epithelial-mesenchymal-transition-in-clear-cell-renal-cell-carcinoma
#16
Li Ning, Zhiguo Li, Dianjun Wei, Haiyan Chen, Chao Yang
BACKGROUND: The long non-coding RNAs (lncRNAs) are emerging as important regulators in cancer progression. Clear cell renal cell carcinoma (ccRCC) is one of the most common urological cancers with poor prognosis. In this study, we examined the functional role of the lncRNA, nuclear enriched abundant transcript 1 (NEAT1) in ccRCC progression. METHODS: We performed quantitative real time PCR and western blotting assays to measure mRNA and protein expression levels, respectively...
February 27, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28260109/absence-of-malat1-does-not-prevent-den-induced-hepatocarcinoma-in-mice
#17
Stéphanie Miard, Marie-Josée Girard, Philippe Joubert, Sophie Carter, Amy Gonzales, Huiping Guo, Benjamin Morpurgo, Louise Boivin, Andrei Golovko, Frédéric Picard
Long non-coding RNAs (lncRNA) are key regulators of gene expression both at the transcriptional and post-transcriptional levels. The lncRNA metastasis associated lung adenocarcinoma transcript 1 (Malat1) is overexpressed in many types of cancer, including hepatocarcinoma, and induces cell proliferation in several cell lines in vitro. However, the direct causal effects of Malat1 on hepatocyte proliferation and liver carcinogenesis in vivo are not fully understood. To better determine the contribution of Malat1 to hepatocarcinoma oncogenesis, this study was aimed at testing the hypothesis that its absence confers resistance to the development of liver tumors...
February 20, 2017: Oncology Reports
https://www.readbyqxmd.com/read/28259935/expression-of-cyclooxygenase-2-is-correlated-with-lncrna-cox-2-in-cirrhotic-mice-induced-by-carbon-tetrachloride
#18
Shi-Hang Tang, Jin-Hang Gao, Shi-Lei Wen, Huan Tong, Zhao-Ping Yan, Rui Liu, Cheng-Wei Tang
Multiple long non-coding RNAs (lncRNAs) have been demonstrated to be involved in liver disease. Increased cyclooxygenase-2 (COX‑2) levels have also been reported to be involved in the progression of liver cirrhosis. In the present study, the correlations between lncRNA‑COX‑2 RNA expression levels, COX‑2 mRNA expression levels and liver fibrosis were examined. Liver fibrosis was induced by intraperitoneal injection of carbon tetrachloride (CCl4) in mice for 2 months (CCl4‑2M) or 3 months (CCl4‑3M)...
February 2, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28255113/-multiple-lncrnas-affect-the-incidence-and-%C3%A2-development-of-melanoma
#19
Han Yan, Dan Tan, Pan Xie, Zhaoqian Liu, Xi Li
To find the relationship between long non-coding RNA (lncRNA) based on data mining methods.
 Methods: We use a whole genome mRNA expression data set (GSE15605) from the gene expression ominibus database to find the lncRNAs which relate to melanoma.
 Results: Four lncRNAs (LINC01213, PGM5-AS1, LINC01133 and LOC284578) were significantly associated with the incidence and development of melanoma. Meanwhile, LINC01213, LINC01133 and LOC284578 were correlated with BRAF mutation, and PGM5-AS1 was related to NRAS mutation...
February 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/28251479/changes-in-lncrnas-and-related-genes-in-%C3%AE-thalassemia-minor-and-%C3%AE-thalassemia-major
#20
Jing Ma, Fei Liu, Xin Du, Duan Ma, Likuan Xiong
β-thalassemia is caused by β-globin gene mutations. However, heterogeneous phenotypes were found in individuals with same genotype, and still undescribed mechanism underlies such variation. We collected blood samples from 30 β-thalassemia major, 30 β-thalassemia minor patients, and 30 matched normal controls. Human lncRNA Array v2.0 (8 × 60 K, Arraystar) was used to detect changes in long non-coding RNAs (lncRNAs) and mRNAs in three samples each from β-thalassemia major, β-thalassemia minor, and control groups...
March 2, 2017: Frontiers of Medicine
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